Merge pull request #186 from desihub/smooth_cont

rewrite of the smooth continuum algorithm for speed and stability
desihub · Oct 30, 2024 · 4f02981 · 4f02981
2 parents bdec78b + 9f9269c
commit 4f02981
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diff --git a/doc/changes.rst b/doc/changes.rst
@@ -5,6 +5,7 @@ Change Log
 3.0.0 (not released yet)
 ------------------------
 
+* Rewrite of the smooth continuum and continuum-flux algorithms [`PR #186`_].
 * Miscellaneous bug fixes [`PR #185`_].
 * Use Numba-based Resolution implementation with faster multiply.
   Also tweak parameters of continuum least_squares optimizer for
@@ -20,6 +21,8 @@ Change Log
 .. _`PR #180`: https://github.com/desihub/fastspecfit/pull/180
 .. _`PR #181`: https://github.com/desihub/fastspecfit/pull/181
 .. _`PR #185`: https://github.com/desihub/fastspecfit/pull/185
+.. _`PR #186`: https://github.com/desihub/fastspecfit/pull/186
+
 
 2.5.2 (2024-04-28)
 ------------------

diff --git a/doc/fastspec.rst b/doc/fastspec.rst
@@ -99,9 +99,9 @@ Name                         Type         Units                         Descript
                        SNR_B      float32                               Median signal-to-noise ratio per pixel in *b* camera.
                        SNR_R      float32                               Median signal-to-noise ratio per pixel in *r* camera.
                        SNR_Z      float32                               Median signal-to-noise ratio per pixel in *z* camera.
-                SMOOTHCORR_B      float32                       percent Mean value of the smooth continuum correction divided by the best-fitting continuum model in the *b* camera.
-                SMOOTHCORR_R      float32                       percent Mean value of the smooth continuum correction divided by the best-fitting continuum model in the *r* camera.
-                SMOOTHCORR_Z      float32                       percent Mean value of the smooth continuum correction divided by the best-fitting continuum model in the *z* camera.
+                SMOOTHCORR_B      float32                       percent Mean value of the smooth continuum correction relative to the data in the *b* camera.
+                SMOOTHCORR_R      float32                       percent Mean value of the smooth continuum correction relative to the data in the *r* camera.
+                SMOOTHCORR_Z      float32                       percent Mean value of the smooth continuum correction relative to the data in the *z* camera.
                        VDISP      float32                        km / s Stellar velocity dispersion.
                   VDISP_IVAR      float32                      s2 / km2 Inverse variance of VDISP.
                           AV      float32                           mag Attenuation of the integrated stellar population.

diff --git a/py/fastspecfit/continuum.py b/py/fastspecfit/continuum.py
diff --git a/py/fastspecfit/data/emlines.ecsv b/py/fastspecfit/data/emlines.ecsv
@@ -36,7 +36,7 @@ name restwave patch isbalmer ishelium isbroad isstrong nicename plotgroup
        civ_1549   1549.06      d   False  False True   True  CIV-$\lambda$1549+HeII-$\lambda$1640                         civ_1549_heii_1640
       heii_1640   1640.42      e   False  True  True   False CIV-$\lambda$1549+HeII-$\lambda$1640                         civ_1549_heii_1640
      aliii_1857   1857.40      f   False  False True   False AlIII-$\lambda$1857+SiIII]-$\lambda$1892+CIII]-$\lambda$1908 aliii_1857_siliii_1892_ciii_1908
-    siliii_1892   1892.03      f   False  False True   False AlIII-$\lambda$1857+SiIII]-$\lambda$1892+CIII]-$\lambda$1908 aliii_1857_siliii_1892_ciii_1908
+    siliii_1892   1892.03      f   False  False True   True  AlIII-$\lambda$1857+SiIII]-$\lambda$1892+CIII]-$\lambda$1908 aliii_1857_siliii_1892_ciii_1908
       ciii_1908   1908.73      f   False  False True   True  AlIII-$\lambda$1857+SiIII]-$\lambda$1892+CIII]-$\lambda$1908 aliii_1857_siliii_1892_ciii_1908
       mgii_2796   2796.352     g   False  False True   True  MgII-$\lambda\lambda$2796,2803                               mgii_2796_2803
       mgii_2803   2803.530     g   False  False True   True  MgII-$\lambda\lambda$2796,2803                               mgii_2796_2803

diff --git a/py/fastspecfit/emlines.py b/py/fastspecfit/emlines.py
@@ -422,7 +422,7 @@ def _initial_guesses_and_bounds(self, linepix, coadd_flux, contpix=None,
         from fastspecfit.util import quantile, median
 
         initials = np.empty(len(self.param_table), dtype=np.float64)
-        bounds   = np.empty((len(self.param_table), 2), dtype=np.float64)
+        bounds = np.empty((len(self.param_table), 2), dtype=np.float64)
 
         # a priori initial guesses and bounds
         minsigma_broad = 1. # 100.
@@ -927,7 +927,7 @@ def get_boundaries(A, v_lo, v_hi):
 
             cmed, civar = 0., 0.
             if len(borderindx) >= nminpix: # require at least XX pixels to get the continuum level
-                clipflux, _, _ = sigmaclip(specflux_nolines_s[borderindx], low=3, high=3)
+                clipflux, _ = sigmaclip(specflux_nolines_s[borderindx], low=3, high=3)
 
                 if len(clipflux) > 0:
                     clo, cmed, chi = quantile(clipflux, (0.25, 0.50, 0.75))
@@ -1316,7 +1316,7 @@ def emline_specfit(data, result, continuummodel, smooth_continuum,
     dwave   = np.round(dwave, decimals=3)
 
     npix = int(np.round((maxwave-minwave)/dwave)) + 1
-    modelwave = minwave + dwave * np.arange(npix)
+    modelwave = minwave + dwave * np.arange(npix, dtype=np.float64)
 
     wavesrt = np.argsort(emlinewave)
     sorted_waves = emlinewave[wavesrt]